BN2003 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.6206e-05 3.8141e-04
Layer 3 1.8873e-05 4.8479e-03
Layer 5 5.6467e-05 3.3496e-04
Layer 2 9.0906e-05 1.9455e-02
Layer 6 3.3968e-04 3.8499e-03
Layer 1 4.6064e-01 4.2853e-01
WM 9.9257e-01 6.7798e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
PRKAR1B Expression Distribution
Gene Specificity Score (GSS)
PRKAR1B GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
PRKAR1B Layer 5 3.2051 0.8001
PCSK1N Layer 5 2.8027 0.7926
TLE5 Layer 5 2.6777 0.7918
NGRN Layer 5 2.8965 0.7917
LDHB Layer 5 2.9160 0.7902
PPP2R1A Layer 5 2.8252 0.7843
RPL7A Layer 5 2.8223 0.7839
NEFL Layer 5 2.9834 0.7838
BASP1 Layer 5 2.7715 0.7829
TUBB4A Layer 5 2.7539 0.7825
VAMP2 Layer 5 2.7969 0.7824
UQCRH Layer 5 2.9668 0.7820
KIF1A Layer 5 2.6484 0.7814
UBC Layer 5 2.5000 0.7813
TSPAN7 Layer 5 2.8770 0.7806
NDRG4 Layer 5 3.2012 0.7798
SERPINI1 Layer 5 3.0059 0.7798
ATP1B1 Layer 5 2.6367 0.7795
MORF4L1 Layer 5 2.7422 0.7789
SRP14 Layer 5 2.7822 0.7788
GAP43 Layer 5 2.8652 0.7782
PEBP1 Layer 5 2.7246 0.7778
ENO2 Layer 5 3.0117 0.7777
RPL8 Layer 5 2.7188 0.7764
COX6C Layer 5 2.9531 0.7763
GPX4 Layer 5 2.7715 0.7758
EIF1 Layer 5 2.5723 0.7755
TSC22D1 Layer 4 2.7246 0.7754
USP22 Layer 4 2.7275 0.7749
FAIM2 Layer 5 2.9834 0.7749
GDI1 Layer 5 2.8086 0.7738
NORAD Layer 5 2.7480 0.7738
DYNLRB1 Layer 5 2.8516 0.7734
RAC1 Layer 5 2.6602 0.7731
ATP2B2 Layer 4 2.6455 0.7730
GNB1 Layer 5 2.8145 0.7730
RNF11 Layer 6 2.5508 0.7723
RPL10 Layer 5 2.6426 0.7721
ATP1A1 Layer 5 2.8145 0.7721
PKM Layer 5 2.9414 0.7719
ATP5MPL Layer 5 2.9727 0.7717
TSPYL1 Layer 5 2.7715 0.7716
SERINC1 Layer 5 2.9277 0.7714
ATP6V0C Layer 5 2.7969 0.7713
DNM1 Layer 5 2.9863 0.7712
GTF2I Layer 5 2.5195 0.7712
STXBP1 Layer 5 2.8457 0.7711
CFL1 Layer 5 2.9219 0.7711
NDFIP1 Layer 5 2.9531 0.7709
STMN1 Layer 5 3.0059 0.7708

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN2003
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN2003_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN2003/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN2003/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN2003/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN2003/report/PD/BN2003_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN2003/report/PD/BN2003_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 10:41:40
  • Number of Processes: 10
  • Spending Time: 0h 3m